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-rw-r--r--gn3/api/gemma.py58
-rw-r--r--tests/integration/test_gemma.py109
2 files changed, 0 insertions, 167 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index ed698d3..21c4cf5 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -26,64 +26,6 @@ def get_version():
return jsonify(run_cmd(f"{gemma_cmd} -v | head -n 1"))
-# This is basically extracted from genenetwork2
-# wqflask/wqflask/marker_regression/gemma_ampping.py
-@gemma.route("/k-gwa-computation", methods=["POST"])
-def run_gemma():
- """Generates a command for generating K-Values and then later, generate a GWA
-command that contains markers. These commands are queued; and the expected
-file output is returned.
-
- """
- data = request.get_json()
- app_defaults = current_app.config
- __hash = generate_hash_of_string(f"{data.get('genofile_name')}_"
- ''.join(data.get("values", "")))
- gemma_kwargs = {
- "geno_filename":
- os.path.join(app_defaults.get("GENODIR"), "bimbam",
- f"{data.get('geno_filename')}"),
- "trait_filename":
- generate_pheno_txt_file(
- tmpdir=app_defaults.get("TMPDIR"),
- values=data.get("values"),
- # Generate this file on the fly!
- trait_filename=(f"{data.get('dataset_groupname')}_"
- f"{data.get('trait_name')}_"
- f"{__hash}.txt"))
- }
- gemma_wrapper_kwargs = {}
- if data.get("loco"):
- gemma_wrapper_kwargs["loco"] = f"--input {data.get('loco')}"
- k_computation_cmd = generate_gemma_computation_cmd(
- gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"),
- gemma_wrapper_kwargs={"loco": f"--input {data.get('loco')}"},
- gemma_kwargs=gemma_kwargs,
- output_file=(f"{app_defaults.get('TMPDIR')}/gn2/"
- f"{data.get('dataset_name')}_K_"
- f"{__hash}.json"))
- gemma_kwargs["lmm"] = data.get("lmm", 9)
- gemma_wrapper_kwargs["input"] = (f"{data.get('dataset_name')}_K_"
- f"{__hash}.json")
- gwa_cmd = generate_gemma_computation_cmd(
- gemma_wrapper_kwargs=gemma_wrapper_kwargs,
- gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"),
- gemma_kwargs=gemma_kwargs,
- output_file=(f"{data.get('dataset_name')}_GWA_"
- f"{__hash}.txt"))
- if not all([k_computation_cmd, gwa_cmd]):
- return jsonify(status=128,
- error="Unable to generate cmds for computation!"), 500
- return jsonify(unique_id=queue_cmd(
- conn=redis.Redis(),
- email=data.get("email"),
- job_queue=app_defaults.get("REDIS_JOB_QUEUE"),
- cmd=f"{k_computation_cmd} && {gwa_cmd}"),
- status="queued",
- output_file=(f"{data.get('dataset_name')}_GWA_"
- f"{__hash}.txt"))
-
-
@gemma.route("/status/<unique_id>", methods=["GET"])
def check_cmd_status(unique_id):
"""Given a (url-encoded) UNIQUE-ID which is returned when hitting any of the
diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index bfce37a..7a7f520 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -39,115 +39,6 @@ class GemmaAPITest(unittest.TestCase):
self.assertEqual(response.status_code, 200)
@mock.patch("gn3.api.gemma.redis.Redis")
- @mock.patch("gn3.api.gemma.queue_cmd")
- @mock.patch("gn3.api.gemma.generate_gemma_computation_cmd")
- def test_run_gemma_no_loco(self, mock_gemma_computation_cmd,
- mock_queue_cmd, mock_redis):
- """Test that gemma composes the command correctly without loco"""
- _redis_conn = MockRedis(redis=mock.MagicMock(), hget=mock.MagicMock())
- mock_redis.return_value = _redis_conn
- mock_gemma_computation_cmd.side_effect = [
- ("gemma-wrapper --json -- "
- "-g genofile.txt -p "
- "test.txt -a genofile_snps.txt "
- "-gk > /tmp/gn2/"
- "bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt"),
- ("gemma-wrapper --json --input /tmp/gn2/"
- "bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt -- "
- "-a genofile_snps.txt -lmm 9 "
- "-g genofile.txt -p "
- "test.txt -a genofile_snps.txt "
- "-gk > /tmp/gn2/"
- "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt")
- ]
- mock_queue_cmd.return_value = "my-unique-id"
- response = self.app.post("/api/gemma/k-gwa-computation",
- json={
- "trait_filename": "BXD.txt",
- "geno_filename": "BXD_geno",
- "values": ["X", "N/A", "X"],
- "dataset_groupname": "BXD",
- "trait_name": "Height",
- "email": "me@me.com",
- "dataset_name": "BXD"
- })
- mock_queue_cmd.assert_has_calls([
- mock.call(conn=_redis_conn,
- email="me@me.com",
- job_queue="GN3::job-queue",
- cmd=("gemma-wrapper --json -- -g "
- "genofile.txt -p test.txt "
- "-a genofile_snps.txt -gk > "
- "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt "
- "&& gemma-wrapper --json --input "
- "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt"
- " -- -a genofile_snps.txt -lmm 9 -g "
- "genofile.txt -p test.txt "
- "-a genofile_snps.txt "
- "-gk > "
- "/tmp/gn2/"
- "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt"))
- ])
- # mock_pheno_txt_file.return_value = "/tmp/gn2/BXD_6OBEPW."
- self.assertEqual(
- response.get_json(), {
- "unique_id": 'my-unique-id',
- "status": "queued",
- "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt"
- })
-
- @mock.patch("gn3.api.gemma.redis.Redis")
- @mock.patch("gn3.api.gemma.queue_cmd")
- def test_run_gemma_with_loco(self, mock_queue_cmd, mock_redis):
- """Test that gemma composes the command correctly with loco"""
- _redis_conn = MockRedis(redis=mock.MagicMock(), hget=mock.MagicMock())
- mock_redis.return_value = _redis_conn
- mock_queue_cmd.return_value = "my-unique-id"
- response = self.app.post("/api/gemma/k-gwa-computation",
- json={
- "trait_filename":
- os.path.abspath(
- os.path.join(
- os.path.dirname(__file__),
- "test_data/")),
- "geno_filename":
- "BXD_geno.txt.gz",
- "values": ["X", "N/A", "X"],
- "dataset_groupname":
- "BXD",
- "trait_name":
- "Height",
- "email":
- "me@me.com",
- "dataset_name":
- "BXD",
- "loco":
- "1,2,3,4,5,6"
- })
- mock_queue_cmd.called_with(
- conn=_redis_conn,
- email="me@me.com",
- job_queue="GN3::job-queue",
- cmd=("gemma-wrapper --json -- -g "
- "genofile.txt -p test.txt "
- "-a genofile_snps.txt -gk > "
- "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt "
- "&& gemma-wrapper --json --input "
- "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt"
- " -- -a genofile_snps.txt -lmm 9 -g "
- "genofile.txt -p test.txt "
- "-a genofile_snps.txt "
- "-gk > "
- "/tmp/gn2/"
- "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt"))
- self.assertEqual(
- response.get_json(), {
- "unique_id": 'my-unique-id',
- "status": "queued",
- "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt"
- })
-
- @mock.patch("gn3.api.gemma.redis.Redis")
def test_check_cmd_status(self, mock_redis):
"""Test that you can check the status of a given command"""
mock_hget = mock.MagicMock()
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 05:32:50 +0000